You're right. Undone has (at least) two meanings. One is to reverse an action that has already been done, like the "UNDO" command on a computer. To "come undone" literally refers to dressing, specifically to something that is buttoned or fastened or tied. In this context, "come undone" means to come apart, to become unbuttoned, unfastened, or untied. "She had her hair in a ponytail, but the rubber band holding it broke and her hair came undone." That's the literal meaning, It has then been extended to mean "to behave badly, to lose control of ones' self."

Thanks a lot for the answers!

Yes, the meanings are different. In the first example, the meaning of the verb to 'undo' is something like to reverse a process. 'Undo' is a transitive verb. For example, you 'do up' the buttons on your coat, and then you 'undo' them. This sentence basically means "It's too late for us to 'undo' what has happened". It's equivalent to "You can't turn back the clock' - what's done is done, and you can't undo it. In this sentence 'to be undone' is a passive form - the infinitive of the verb 'to be' + the past participle. To 'come undone' is an intransitive verb phrase, used to describe something which happens without the 'agent' of a person doing something. For example, if the buttons on your coat are too small for the buttonholes, they will 'come undone'. In your song lyrics, 'come undone' is used figuratively. My guess is that it means something like 'fall apart' emotionally.